Thank you so much for clarifying that. I have re-done the analysis as suggested using ‘–p-trunc-len-f’ set as 110 and
--p-trunc-len-r set as 150.
Please see the attached results denoising-stats-dada2.qzv (1.2 MB)
Could you please share your thoughts on what are good benchmarks for:
- percentage of input passed filter
- percentage of input merged
- percentage of input non-chimeric
Also, what are your suggestions for troubleshooting samples with low values?
In our data (attached), the average percentage percentage of input that passed filtering was 80%; the average percentage of input merged was 32% and; and the average percentage of input non-chimeric was also 32%.
Although the percentage of input that passed the filter was not bad, merging was really low (over 40% of the samples had less than 10% of the input merged).
I would appreciate any suggestions on how to proceed to troubleshoot our data.
Thanks again for you help!!